Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/jobs/xb/inputs/xjy Working: n-9-21.cluster.ucsf.bkslab.org:/scratch/xiaobo/49269/xjy-8068961.259 Result: /scratch/xiaobo/49269/xjy-8068961.259 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/jobs/xb/outputs/xjy 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/jobs/xb/inputs/xjy mkdir: created directory `/scratch/xiaobo/49269' mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259' /scratch/xiaobo/49269/xjy-8068961.259 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/jobs/xb/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/49269/xjy-8068961.259/working' mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/protonate' Storing results in /scratch/xiaobo/49269/xjy-8068961.259/finished Working in /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 /scratch/xiaobo/49269/xjy-8068961.259/working/protonate /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Using inputs as protomers/tautomers. No processing done 21 substances and 40 protomers extracted Coalesing and merging protomers 40 protomers generated for 40 compounds Checking for new stereocenters and expanding 40 protomers after new stereo-center expansion /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Bulk generating 3D conformations all protomers in /scratch/xiaobo/49269/xjy-8068961.259/working/3D mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/49269/xjy-8068961.259/working/protonate/xjy-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' 41 3D conformations generated for 40 compounds Building ZINC000014946695 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building' mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000014946695 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/1 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)OCC(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N[C@@H](CCCC(=O)O)C(N)=O) `ZINC000014946695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000014946695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 29 is the cov attach 4 29 0 4 29 1 4 29 2 3 29 2 32 to be deleted 33 to be deleted 34 to be deleted natoms 96 natoms 95 natoms 94 natoms 93 names: ZINC000014946695 none CCC[C@H](NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)OCC(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N[C@@H](CCCC(=O)O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 1, 11, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 5, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 19, 29, 32, 32, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 19, 19, 29, 29, 96, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82] set([22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 64, 65, 66, 67, 68, 69, 70, 71, 72, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92]) total number of confs: 306 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000014946695 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/finished' Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000014946695 Building ZINC000025986807 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025986807 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/2 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025986807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986807 none CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 11, 14, 6, 6, 3, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 3, 7, 11, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 11, 11, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/3 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025986807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986807 none CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 8, 11, 4, 4, 2, 1, 2, 2, 4, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 6, 10, 17, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 4, 4, 4, 5, 5, 5, 5, 5, 2, 6, 6, 10, 10, 17, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000025986807 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 Building ZINC000025986807 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025986807 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 2) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025986807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986807 none CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 11, 14, 6, 6, 3, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 3, 7, 11, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 11, 11, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 3) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025986807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986807 none CCN1[C@@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 8, 11, 4, 4, 2, 1, 2, 2, 4, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 6, 10, 17, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 4, 4, 4, 5, 5, 5, 5, 5, 2, 6, 6, 10, 10, 17, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000025986807 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986807 Building ZINC000025986815 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025986815 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/4 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025986815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986815 none CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 3, 6, 3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 11, 11, 21, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 21, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/5 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025986815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986815 none CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 4, 4, 2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 8, 9, 18, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 9, 9, 18, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000025986815 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 Building ZINC000025986815 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025986815 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 4) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025986815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986815 none CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 3, 6, 3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 11, 11, 21, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 21, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 5) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3) `ZINC000025986815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025986815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC000025986815 none CCN1[C@H](C(=O)N[C@@H](Cc2ccccc2)[C@]([O-])([SiH3])C(=O)NCCNS(C)(=O)=O)Cc2cc3c(cc2S1(=O)=O)OCCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'H', '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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 4, 4, 2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 8, 9, 18, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 9, 9, 18, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 64, 65, 66, 67, 68, 69, 70, 71, 72]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000025986815 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000025986815 Building ZINC000027077048 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000027077048 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/6 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C) `ZINC000027077048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000027077048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 34 is the cov attach 4 34 0 4 34 1 4 34 2 3 34 2 37 to be deleted 38 to be deleted 39 to be deleted natoms 90 natoms 89 natoms 88 natoms 87 names: ZINC000027077048 none CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 5, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 10, 5, 10, 5, 5, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 10, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 36, 18, 18, 15, 5, 4, 4, 4, 2, 2, 2, 6, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11] 300 rigid atoms, others: [34, 35, 36, 27, 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, 26, 31, 32, 33, 37, 38, 39, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/7 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C) `ZINC000027077048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000027077048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 34 is the cov attach 4 34 0 4 34 1 4 34 2 3 34 2 37 to be deleted 38 to be deleted 39 to be deleted natoms 90 natoms 89 natoms 88 natoms 87 names: ZINC000027077048 none CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 5, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 11, 5, 11, 5, 5, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 11, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 46, 23, 23, 16, 5, 4, 4, 4, 2, 1, 1, 3, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12] 300 rigid atoms, others: [32, 33, 34, 67, 68, 37, 38, 39, 70, 35, 36, 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, 22, 23, 24, 25, 26, 40, 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, 69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000027077048 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 Building ZINC000027077048 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000027077048 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 6) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C) `ZINC000027077048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000027077048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 34 is the cov attach 4 34 0 4 34 1 4 34 2 3 34 2 37 to be deleted 38 to be deleted 39 to be deleted natoms 90 natoms 89 natoms 88 natoms 87 names: ZINC000027077048 none CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 5, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 10, 5, 10, 5, 5, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 10, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 36, 18, 18, 15, 5, 4, 4, 4, 2, 2, 2, 6, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11] 300 rigid atoms, others: [34, 35, 36, 27, 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, 26, 31, 32, 33, 37, 38, 39, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 7) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C) `ZINC000027077048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000027077048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 34 is the cov attach 4 34 0 4 34 1 4 34 2 3 34 2 37 to be deleted 38 to be deleted 39 to be deleted natoms 90 natoms 89 natoms 88 natoms 87 names: ZINC000027077048 none CC(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)[C@]([O-])([SiH3])C(=O)NCCc1ccccc1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 7, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 6, 6, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 5, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 11, 5, 11, 5, 5, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 11, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 46, 23, 23, 16, 5, 4, 4, 4, 2, 1, 1, 3, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12] 300 rigid atoms, others: [32, 33, 34, 67, 68, 37, 38, 39, 70, 35, 36, 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, 22, 23, 24, 25, 26, 40, 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, 69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000027077048 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000027077048 Building ZINC000028360492 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360492 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/8 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360492 none CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 18, 18, 18, 32, 32, 36, 36, 36, 48, 39, 49, 50, 50, 50, 50, 50, 50, 32, 33, 33, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 18, 36, 48, 48, 48, 48, 49, 47, 50, 50, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 50 rigid atoms, others: [96, 97, 98, 3, 100, 99, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 313 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/9 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360492 none CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 2, 2, 4, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 17, 17, 17, 31, 31, 34, 34, 34, 45, 37, 48, 50, 50, 50, 50, 50, 50, 31, 32, 32, 11, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 34, 45, 45, 45, 45, 48, 43, 50, 50, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360492 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 Building ZINC000028360492 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360492 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 8) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360492 none CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 18, 18, 18, 32, 32, 36, 36, 36, 48, 39, 49, 50, 50, 50, 50, 50, 50, 32, 33, 33, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 18, 36, 48, 48, 48, 48, 49, 47, 50, 50, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 50 rigid atoms, others: [96, 97, 98, 3, 100, 99, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 313 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 9) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360492 none CCC[C@@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 2, 2, 4, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 17, 17, 17, 31, 31, 34, 34, 34, 45, 37, 48, 50, 50, 50, 50, 50, 50, 31, 32, 32, 11, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 34, 45, 45, 45, 45, 48, 43, 50, 50, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360492 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360492 Building ZINC000028360498 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360498 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/10 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360498 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 8, 8, 13, 13, 13, 26, 26, 31, 31, 31, 44, 36, 47, 50, 50, 50, 50, 50, 50, 26, 28, 28, 8, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 31, 44, 44, 44, 44, 47, 43, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/11 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360498 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 9, 9, 12, 12, 12, 22, 22, 26, 26, 26, 44, 31, 47, 50, 50, 50, 50, 50, 50, 22, 25, 25, 9, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 44, 44, 44, 44, 42, 47, 50, 50, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360498 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 Building ZINC000028360498 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360498 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 10) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360498 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 8, 8, 13, 13, 13, 26, 26, 31, 31, 31, 44, 36, 47, 50, 50, 50, 50, 50, 50, 26, 28, 28, 8, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 31, 44, 44, 44, 44, 47, 43, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 11) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360498 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 9, 9, 12, 12, 12, 22, 22, 26, 26, 26, 44, 31, 47, 50, 50, 50, 50, 50, 50, 22, 25, 25, 9, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 44, 44, 44, 44, 42, 47, 50, 50, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360498 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360498 Building ZINC000028360503 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360503 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/12 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360503 none CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 21, 21, 21, 36, 36, 36, 36, 36, 49, 45, 49, 50, 50, 50, 50, 50, 50, 36, 36, 36, 12, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 21, 36, 49, 49, 49, 49, 49, 49, 50, 50, 36, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 5, 47, 48, 49] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 289 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/13 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360503 none CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 32, 32, 32, 39, 39, 39, 39, 39, 44, 44, 46, 50, 50, 50, 50, 50, 50, 39, 39, 39, 17, 25, 25, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 32, 39, 44, 44, 44, 44, 46, 46, 50, 50, 39, 39, 39, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360503 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 Building ZINC000028360503 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360503 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 12) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360503 none CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 21, 21, 21, 36, 36, 36, 36, 36, 49, 45, 49, 50, 50, 50, 50, 50, 50, 36, 36, 36, 12, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 21, 36, 49, 49, 49, 49, 49, 49, 50, 50, 36, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 5, 47, 48, 49] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 289 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 13) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360503 none CCC[C@@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 32, 32, 32, 39, 39, 39, 39, 39, 44, 44, 46, 50, 50, 50, 50, 50, 50, 39, 39, 39, 17, 25, 25, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 32, 39, 44, 44, 44, 44, 46, 46, 50, 50, 39, 39, 39, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360503 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360503 Building ZINC000028360510 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360510 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/14 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360510 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 31, 31, 31, 35, 35, 35, 35, 35, 44, 44, 48, 50, 50, 50, 50, 50, 50, 35, 35, 35, 16, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 31, 35, 44, 44, 46, 46, 48, 48, 50, 50, 35, 35, 35, 35, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/15 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360510 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 13, 13, 26, 26, 26, 36, 36, 36, 36, 36, 46, 45, 48, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 46, 46, 47, 47, 48, 48, 50, 50, 36, 36, 36, 36, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 96, 97, 98, 99, 100] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360510 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 Building ZINC000028360510 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028360510 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 14) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028360510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360510 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 31, 31, 31, 35, 35, 35, 35, 35, 44, 44, 48, 50, 50, 50, 50, 50, 50, 35, 35, 35, 16, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 31, 35, 44, 44, 46, 46, 48, 48, 50, 50, 35, 35, 35, 35, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 15) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000028360510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028360510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000028360510 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 13, 13, 26, 26, 26, 36, 36, 36, 36, 36, 46, 45, 48, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 46, 46, 47, 47, 48, 48, 50, 50, 36, 36, 36, 36, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 96, 97, 98, 99, 100] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000028360510 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000028360510 Building ZINC000049757280 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000049757280 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/16 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@@]([O-])([SiH3])C(=O)NCc1ccccc1) `ZINC000049757280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000049757280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 37 is the cov attach 4 37 0 4 37 1 4 37 2 3 37 2 40 to be deleted 41 to be deleted 42 to be deleted natoms 89 natoms 88 natoms 87 natoms 86 names: ZINC000049757280 none CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@@]([O-])([SiH3])C(=O)NCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 12, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 16, 9, 11, 11, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 39, 39, 39, 35, 35, 9, 9, 9, 9, 9, 9, 4, 9, 4, 4, 2, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 18, 35, 35, 35, 35, 39, 39, 117, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 9, 11, 11] 150 rigid atoms, others: [32, 37, 38, 39] 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, 28, 29, 30, 31, 33, 34, 35, 36, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/17 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@]([O-])([SiH3])C(=O)NCc1ccccc1) `ZINC000049757280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000049757280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 37 is the cov attach 4 37 0 4 37 1 4 37 2 3 37 2 40 to be deleted 41 to be deleted 42 to be deleted natoms 89 natoms 88 natoms 87 natoms 86 names: ZINC000049757280 none CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@]([O-])([SiH3])C(=O)NCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 12, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 10, 5, 7, 7, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 51, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 11, 11, 7, 11, 11] 150 rigid atoms, others: [32, 33, 34, 37, 38, 39, 40, 41, 42, 78, 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, 28, 29, 30, 35, 36, 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, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 85]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000049757280 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 Building ZINC000049757280 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000049757280 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 16) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@@]([O-])([SiH3])C(=O)NCc1ccccc1) `ZINC000049757280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000049757280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 37 is the cov attach 4 37 0 4 37 1 4 37 2 3 37 2 40 to be deleted 41 to be deleted 42 to be deleted natoms 89 natoms 88 natoms 87 natoms 86 names: ZINC000049757280 none CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@@]([O-])([SiH3])C(=O)NCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 12, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 16, 9, 11, 11, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 39, 39, 39, 35, 35, 9, 9, 9, 9, 9, 9, 4, 9, 4, 4, 2, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 18, 35, 35, 35, 35, 39, 39, 117, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 9, 11, 11] 150 rigid atoms, others: [32, 37, 38, 39] 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, 28, 29, 30, 31, 33, 34, 35, 36, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 17) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@]([O-])([SiH3])C(=O)NCc1ccccc1) `ZINC000049757280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000049757280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 37 is the cov attach 4 37 0 4 37 1 4 37 2 3 37 2 40 to be deleted 41 to be deleted 42 to be deleted natoms 89 natoms 88 natoms 87 natoms 86 names: ZINC000049757280 none CC(C)[C@H](NC(=O)Cn1ccc(=O)n(CC(=O)O)c1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C(C)C)[C@]([O-])([SiH3])C(=O)NCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 12, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 10, 5, 7, 7, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 51, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 11, 11, 7, 11, 11] 150 rigid atoms, others: [32, 33, 34, 37, 38, 39, 40, 41, 42, 78, 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, 28, 29, 30, 35, 36, 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, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 85]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000049757280 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000049757280 Building ZINC000096904165 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000096904165 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/18 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000096904165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904165 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 17, 17, 31, 31, 31, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 17, 22, 22, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 31, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/19 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000096904165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904165 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 23, 23, 23, 35, 35, 36, 36, 36, 49, 47, 49, 50, 50, 50, 50, 50, 50, 35, 36, 36, 13, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 23, 36, 49, 49, 49, 49, 49, 49, 50, 50, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 49, 56, 57, 58, 59, 60, 61, 62] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 256 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000096904165 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 Building ZINC000096904165 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000096904165 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 18) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000096904165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904165 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 17, 17, 31, 31, 31, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 17, 22, 22, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 31, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 19) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000096904165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904165 none CCC[C@H](NC(=O)[C@@H]1[C@@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 23, 23, 23, 35, 35, 36, 36, 36, 49, 47, 49, 50, 50, 50, 50, 50, 50, 35, 36, 36, 13, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 23, 36, 49, 49, 49, 49, 49, 49, 50, 50, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 49, 56, 57, 58, 59, 60, 61, 62] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 256 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000096904165 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904165 Building ZINC000096904166 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000096904166 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/20 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000096904166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904166 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 17, 17, 17, 34, 34, 42, 42, 42, 50, 49, 50, 50, 50, 50, 50, 50, 50, 34, 38, 38, 10, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 6, 6, 17, 42, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/21 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000096904166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904166 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 41, 41, 42, 42, 42, 48, 45, 48, 50, 50, 50, 50, 50, 50, 41, 41, 41, 11, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 24, 42, 48, 48, 48, 48, 48, 48, 50, 50, 41, 41, 41, 41, 41, 41, 41, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1] 50 rigid atoms, others: [96, 97, 98, 3, 100, 99, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000096904166 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 Building ZINC000096904166 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000096904166 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 20) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000096904166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904166 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 17, 17, 17, 34, 34, 42, 42, 42, 50, 49, 50, 50, 50, 50, 50, 50, 50, 34, 38, 38, 10, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 6, 6, 17, 42, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 3, 47] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 21) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN) `ZINC000096904166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000096904166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 47 is the cov attach 4 47 0 4 47 1 4 47 2 3 47 2 50 to be deleted 51 to be deleted 52 to be deleted natoms 104 natoms 103 natoms 102 natoms 101 names: ZINC000096904166 none CCC[C@H](NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)[C@@H](NC(=O)CCCCc1nnn[nH]1)C(C)C)C(C)C)[C@]([O-])([SiH3])C(=O)NC(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 41, 41, 42, 42, 42, 48, 45, 48, 50, 50, 50, 50, 50, 50, 41, 41, 41, 11, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 24, 42, 48, 48, 48, 48, 48, 48, 50, 50, 41, 41, 41, 41, 41, 41, 41, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1] 50 rigid atoms, others: [96, 97, 98, 3, 100, 99, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000096904166 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000096904166 Building ZINC000103259469 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103259469 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/22 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1) `ZINC000103259469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103259469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC000103259469 none CNC(=O)[C@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 3, 3, 5, 5, 5, 36, 37, 37, 37, 37, 37, 37, 37, 41, 41, 41, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 4, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 37, 37, 37, 37, 37, 37, 43, 43, 43, 43, 43, 43, 43, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/23 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1) `ZINC000103259469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103259469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC000103259469 none CNC(=O)[C@@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 4, 30, 35, 35, 35, 35, 35, 35, 35, 44, 44, 44, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 3, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 35, 35, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000103259469 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 Building ZINC000103259469 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103259469 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 22) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CNC(=O)[C@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1) `ZINC000103259469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103259469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC000103259469 none CNC(=O)[C@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 3, 3, 5, 5, 5, 36, 37, 37, 37, 37, 37, 37, 37, 41, 41, 41, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 4, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 37, 37, 37, 37, 37, 37, 43, 43, 43, 43, 43, 43, 43, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 23) grep: /scratch/xiaobo/49269/xjy-8068961.259/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: CNC(=O)[C@@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1) `ZINC000103259469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103259469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC000103259469 none CNC(=O)[C@@]([O-])([SiH3])[C@H](NC(=O)[C@@H]1CC[C@H]2CN(S(=O)(=O)Cc3ccccc3)CC(=O)N21)[C@H]1CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 4, 30, 35, 35, 35, 35, 35, 35, 35, 44, 44, 44, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 3, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 35, 35, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000103259469 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000103259469 Building ZINC000199531016 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000199531016 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/24 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1) `ZINC000199531016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000199531016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 29 is the cov attach 4 29 0 4 29 1 4 29 2 3 29 2 32 to be deleted 33 to be deleted 34 to be deleted natoms 88 natoms 87 natoms 86 natoms 85 names: ZINC000199531016 none CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 7, 7, 7, 8, 8, 8, 8, 8, 12, 12, 12, 13, 13, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 8, 12, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [32, 33, 34, 3, 71, 29, 30, 31] set([0, 1, 2, 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, 35, 36, 37, 38, 39, 40, 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, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/25 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1) `ZINC000199531016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000199531016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 29 is the cov attach 4 29 0 4 29 1 4 29 2 3 29 2 32 to be deleted 33 to be deleted 34 to be deleted natoms 88 natoms 87 natoms 86 natoms 85 names: ZINC000199531016 none CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 15, 15, 15, 15, 15, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 5, 9, 9, 9, 9, 13, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [3, 29, 30, 31] set([0, 1, 2, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000199531016 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 Building ZINC000199531016 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000199531016 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 24) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1) `ZINC000199531016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000199531016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 29 is the cov attach 4 29 0 4 29 1 4 29 2 3 29 2 32 to be deleted 33 to be deleted 34 to be deleted natoms 88 natoms 87 natoms 86 natoms 85 names: ZINC000199531016 none CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 7, 7, 7, 8, 8, 8, 8, 8, 12, 12, 12, 13, 13, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 8, 12, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [32, 33, 34, 3, 71, 29, 30, 31] set([0, 1, 2, 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, 35, 36, 37, 38, 39, 40, 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, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 25) grep: /scratch/xiaobo/49269/xjy-8068961.259/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1) `ZINC000199531016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000199531016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 29 is the cov attach 4 29 0 4 29 1 4 29 2 3 29 2 32 to be deleted 33 to be deleted 34 to be deleted natoms 88 natoms 87 natoms 86 natoms 85 names: ZINC000199531016 none CC(C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)c1ccccc1)C(C)(C)C)[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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] dock color type numbers: [7, 7, 7, 9, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 15, 15, 15, 15, 15, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 5, 9, 9, 9, 9, 13, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [3, 29, 30, 31] set([0, 1, 2, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Finished preparing ZINC000199531016 Recording results /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Appending to /scratch/xiaobo/49269/xjy-8068961.259/finished/xjy.* 1: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/1.* 0: /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016/0.* Removing working files in /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000199531016 Building ZINC000963797656 mkdir: created directory `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000963797656 mkdir: created directory `0' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656/0 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/26 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1OC)[C@H]([C@H](O)[C@H](O)[C@H](CO)O[C@@H]1OC[C@H](O)[C@@H](O)[C@@H]1O)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccccc31)CC2) `ZINC000963797656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000963797656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 39 is the cov attach 4 39 0 4 39 1 4 39 2 3 39 2 42 to be deleted 43 to be deleted 44 to be deleted natoms 83 natoms 82 natoms 81 natoms 80 names: ZINC000963797656 none COc1ccc2c(c1OC)[C@H]([C@H](O)[C@H](O)[C@H](CO)O[C@@H]1OC[C@H](O)[C@@H](O)[C@@H]1O)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccccc31)CC2 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', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 7, 12, 5, 7, 5, 12, 12, 5, 7, 12, 5, 5, 7, 12, 5, 7, 12, 5, 7, 12, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 6, 6, 6, 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, 4, 7, 7, 4, 7, 7, 7, 4, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 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] 6 hydrogens need rotated 36450 conformations in input total number of sets (complete confs): 36450 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 6, 3, 3, 3, 6, 6, 6, 9, 9, 9, 14, 14, 17, 14, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 6, 6, 6, 3, 3, 6, 6, 6, 18, 27, 17, 17, 51, 26, 26, 78, 78, 78, 4, 4, 4, 4, 4, 3, 3, 3, 3] 36450 Total number of coords too high 2916000 > 1000000 splitting original input conformations into 4 parts (current depth: 1 ) total number of sets (complete confs): 9112 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 6, 9, 6, 6, 18, 7, 7, 21, 21, 21, 3, 3, 3, 3, 3, 2, 2, 2, 2] 9112 rigid atoms, others: [40, 41, 37, 39] 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 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, 74, 75, 76, 77, 78, 79]) total number of confs: 140 number of broken/clashed sets: 5670 ./output.1.db2in.mol2.db2.gz file written out Cleaning up total number of sets (complete confs): 9112 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 2, 2, 2, 3, 3, 3, 5, 5, 5, 7, 7, 9, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 5, 5, 5, 2, 2, 5, 5, 5, 9, 15, 9, 9, 27, 10, 10, 30, 30, 30, 4, 4, 4, 4, 4, 2, 2, 2, 2] 9112 rigid atoms, others: [40, 41, 37, 39] 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 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, 74, 75, 76, 77, 78, 79]) total number of confs: 207 number of broken/clashed sets: 5084 ./output.1.db2in.mol2.db2.gz file written out Cleaning up total number of sets (complete confs): 9112 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 5, 2, 2, 2, 3, 3, 3, 5, 5, 5, 8, 8, 9, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 9, 15, 9, 9, 27, 12, 12, 36, 36, 36, 4, 4, 4, 4, 4, 2, 2, 2, 2] 9112 rigid atoms, others: [40, 41, 37, 39] 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 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, 74, 75, 76, 77, 78, 79]) total number of confs: 225 number of broken/clashed sets: 4231 ./output.1.db2in.mol2.db2.gz file written out Cleaning up total number of sets (complete confs): 9112 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 6, 3, 3, 3, 6, 6, 6, 8, 8, 8, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 6, 6, 6, 3, 3, 6, 6, 6, 18, 24, 11, 11, 33, 13, 13, 39, 39, 39, 4, 4, 4, 4, 4, 3, 3, 3, 3] 9112 rigid atoms, others: [40, 41, 37, 39] 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 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, 74, 75, 76, 77, 78, 79]) total number of confs: 259 number of broken/clashed sets: 5245 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 mkdir: created directory `1' /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656/1 /scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656 /scratch/xiaobo/49269/xjy-8068961.259/working /scratch/xiaobo/49269/xjy-8068961.259 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/49269/xjy-8068961.259/working/3D/27 `/scratch/xiaobo/49269/xjy-8068961.259/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1OC)[C@H]([C@H](O)[C@H](O)[C@H](CO)O[C@@H]1OC[C@H](O)[C@@H](O)[C@@H]1O)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccccc31)CC2) `ZINC000963797656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000963797656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/49269/xjy-8068961.259/working/building/ZINC000963797656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1